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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:HOOK3-LCN2 (FusionGDB2 ID:37236)

Fusion Gene Summary for HOOK3-LCN2

check button Fusion gene summary
Fusion gene informationFusion gene name: HOOK3-LCN2
Fusion gene ID: 37236
HgeneTgene
Gene symbol

HOOK3

LCN2

Gene ID

84376

3934

Gene namehook microtubule tethering protein 3lipocalin 2
SynonymsHK324p3|MSFI|NGAL|p25
Cytomap

8p11.21

9q34.11

Type of geneprotein-codingprotein-coding
Descriptionprotein Hook homolog 3h-hook3hHK3hook homolog 3neutrophil gelatinase-associated lipocalin25 kDa alpha-2-microglobulin-related subunit of MMP-9migration-stimulating factor inhibitoroncogene 24p3siderocalin LCN2
Modification date2020031320200329
UniProtAcc.

P80188

Ensembl transtripts involved in fusion geneENST00000307602, ENST00000524839, 
ENST00000373017, ENST00000470902, 
ENST00000540948, ENST00000277480, 
ENST00000373013, ENST00000372998, 
Fusion gene scores* DoF score16 X 13 X 9=187211 X 10 X 5=550
# samples 1912
** MAII scorelog2(19/1872*10)=-3.30050911125246
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HOOK3 [Title/Abstract] AND LCN2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHOOK3(42798588)-LCN2(130915379), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneLCN2

GO:0042742

defense response to bacterium

27780864

TgeneLCN2

GO:0097577

sequestering of iron ion

27780864


check buttonFusion gene breakpoints across HOOK3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across LCN2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4STADTCGA-CD-A48C-01AHOOK3chr8

42798588

+LCN2chr9

130915379

+


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Fusion Gene ORF analysis for HOOK3-LCN2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000307602ENST00000373017HOOK3chr8

42798588

+LCN2chr9

130915379

+
5CDS-3UTRENST00000307602ENST00000470902HOOK3chr8

42798588

+LCN2chr9

130915379

+
5CDS-intronENST00000307602ENST00000540948HOOK3chr8

42798588

+LCN2chr9

130915379

+
5CDS-intronENST00000307602ENST00000277480HOOK3chr8

42798588

+LCN2chr9

130915379

+
5CDS-intronENST00000307602ENST00000373013HOOK3chr8

42798588

+LCN2chr9

130915379

+
5CDS-intronENST00000307602ENST00000372998HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-3CDSENST00000524839ENST00000373017HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-3UTRENST00000524839ENST00000470902HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-intronENST00000524839ENST00000540948HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-intronENST00000524839ENST00000277480HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-intronENST00000524839ENST00000373013HOOK3chr8

42798588

+LCN2chr9

130915379

+
intron-intronENST00000524839ENST00000372998HOOK3chr8

42798588

+LCN2chr9

130915379

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000307602HOOK3chr842798588+ENST00000373017LCN2chr9130915379+634600182619145

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000307602ENST00000373017HOOK3chr842798588+LCN2chr9130915379+0.0107504310.9892496

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Fusion Genomic Features for HOOK3-LCN2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
HOOK3chr842798588+LCN2chr9130915378+0.05671470.9432853
HOOK3chr842798588+LCN2chr9130915378+0.05671470.9432853

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for HOOK3-LCN2


check button Go to

FGviewer for the breakpoints of chr8:42798588-chr9:130915379

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.LCN2

P80188

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development (PubMed:12453413, PubMed:27780864, PubMed:20581821). Binds iron through association with 2,3-dihydroxybenzoic acid (2,3-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis (By similarity). Involved in innate immunity; limits bacterial proliferation by sequestering iron bound to microbial siderophores, such as enterobactin (PubMed:27780864). Can also bind siderophores from M.tuberculosis (PubMed:15642259, PubMed:21978368). {ECO:0000250|UniProtKB:P11672, ECO:0000269|PubMed:12453413, ECO:0000269|PubMed:15642259, ECO:0000269|PubMed:20581821, ECO:0000269|PubMed:21978368, ECO:0000269|PubMed:27780864}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneHOOK3chr8:42798588chr9:130915379ENST00000307602+52210_126133.33333333333334719.0DomainCalponin-homology (CH)
TgeneLCN2chr8:42798588chr9:130915379ENST000005409480572_740199.0RegionCarboxymycobactin binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneHOOK3chr8:42798588chr9:130915379ENST00000307602+522167_433133.33333333333334719.0Coiled coilOntology_term=ECO:0000255
HgeneHOOK3chr8:42798588chr9:130915379ENST00000307602+522462_667133.33333333333334719.0Coiled coilOntology_term=ECO:0000255
HgeneHOOK3chr8:42798588chr9:130915379ENST00000307602+522553_718133.33333333333334719.0RegionNote=Required for association with Golgi
TgeneLCN2chr8:42798588chr9:130915379ENST000002774804772_74192.33333333333334177.0RegionCarboxymycobactin binding
TgeneLCN2chr8:42798588chr9:130915379ENST000003730175772_74192.33333333333334199.0RegionCarboxymycobactin binding


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Fusion Gene Sequence for HOOK3-LCN2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>In-frame_ENST00000307602_ENST00000373017_TCGA-CD-A48C-01A_HOOK3_chr8_42798588_+_LCN2_chr9_130915379_length(transcript)=634nt_BP=600nt
CGGTCCCGAGTGAAAGGAGAAGGAGGGGCGCTGGGGGTGACGGTGCGGAGCCGCTGCCAGCGCTGGGCGAGAGTCGGCGGCCGGATCCGA
GGAGCAGGCGGGCCTGAGGCCGAGTCAGCTGCGCGGGCCCCCGGATCCCCCGACAGAGCGGCGGCGGTGTCTGGCCAGGCGGTAGGCGCT
GCCTGGCCGCGGCGGGGAAGATGTTCAGCGTAGAGTCGCTGGAGCGGGCGGAGCTGTGCGAGAGCCTCCTCACTTGGATCCAGACATTTA
ATGTGGATGCACCATGCCAGACCGTGGAAGATTTAACGAATGGGGTTGTGATGGCCCAGGTTCTTCAAAAGATAGATCCTGCATATTTTG
ATGAAAATTGGCTAAACAGAATCAAAACTGAAGTAGGAGATAATTGGAGGCTAAAGATAAGCAATTTAAAGAAAATTTTAAAAGGAATCT
TGGATTATAATCATGAGATTTTAGGACAGCAAATTAATGACTTTACCCTTCCTGATGTGAACCTTATTGGGGAGCATTCTGATGCAGCAG
AGCTTGGAAGGATGCTTCAGCTCATCTTAGGCTGTGCTGTGAACTGTGAACAGAAGCAAGACCAGTGTATCGACGGCTGAGTGCACAGTG

>In-frame_ENST00000307602_ENST00000373017_TCGA-CD-A48C-01A_HOOK3_chr8_42798588_+_LCN2_chr9_130915379_length(amino acids)=145AA_start in transcript=182_stop in transcript=619
MAAAGKMFSVESLERAELCESLLTWIQTFNVDAPCQTVEDLTNGVVMAQVLQKIDPAYFDENWLNRIKTEVGDNWRLKISNLKKILKGIL

--------------------------------------------------------------

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Fusion Gene PPI Analysis for HOOK3-LCN2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for HOOK3-LCN2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for HOOK3-LCN2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHOOK3C0032460Polycystic Ovary Syndrome1CTD_human
HgeneHOOK3C1136382Sclerocystic Ovaries1CTD_human
TgeneLCN2C0022660Kidney Failure, Acute5CTD_human
TgeneLCN2C1565662Acute Kidney Insufficiency5CTD_human
TgeneLCN2C2609414Acute kidney injury5CTD_human
TgeneLCN2C0022658Kidney Diseases4CTD_human
TgeneLCN2C0019193Hepatitis, Toxic2CTD_human
TgeneLCN2C0023893Liver Cirrhosis, Experimental2CTD_human
TgeneLCN2C0860207Drug-Induced Liver Disease2CTD_human
TgeneLCN2C1262760Hepatitis, Drug-Induced2CTD_human
TgeneLCN2C3658290Drug-Induced Acute Liver Injury2CTD_human
TgeneLCN2C4277682Chemical and Drug Induced Liver Injury2CTD_human
TgeneLCN2C4279912Chemically-Induced Liver Toxicity2CTD_human
TgeneLCN2C0002875Cooley's anemia1CTD_human
TgeneLCN2C0003873Rheumatoid Arthritis1CTD_human
TgeneLCN2C0005283beta Thalassemia1CTD_human
TgeneLCN2C0006663Calcinosis1CTD_human
TgeneLCN2C0006826Malignant Neoplasms1CTD_human
TgeneLCN2C0007570Celiac Disease1CTD_human
TgeneLCN2C0011616Contact Dermatitis1CTD_human
TgeneLCN2C0013221Drug toxicity1CTD_human
TgeneLCN2C0018824Heart valve disease1CTD_human
TgeneLCN2C0019025Hemoglobin F Disease1CTD_human
TgeneLCN2C0019188Hepatitis, Animal1CTD_human
TgeneLCN2C0021368Inflammation1CTD_human
TgeneLCN2C0027627Neoplasm Metastasis1CTD_human
TgeneLCN2C0027651Neoplasms1CTD_human
TgeneLCN2C0035222Respiratory Distress Syndrome, Adult1CTD_human
TgeneLCN2C0036341Schizophrenia1PSYGENET
TgeneLCN2C0041755Adverse reaction to drug1CTD_human
TgeneLCN2C0085578Thalassemia Minor1CTD_human
TgeneLCN2C0086692Benign Neoplasm1CTD_human
TgeneLCN2C0162351Contact hypersensitivity1CTD_human
TgeneLCN2C0263628Tumoral calcinosis1CTD_human
TgeneLCN2C0271979Thalassemia Intermedia1CTD_human
TgeneLCN2C0403447Chronic Kidney Insufficiency1CTD_human
TgeneLCN2C0521174Microcalcification1CTD_human
TgeneLCN2C1561643Chronic Kidney Diseases1CTD_human